# lib构建
FROM mambaorg/micromamba:1.5.3-bookworm-slim
# 设置用户为root
USER root
# 设置build中conda激活
ARG MAMBA_DOCKERFILE_ACTIVATE=1
# 设置conda源
COPY .mambarc /root/.mambarc
# 复制conda环境配置
COPY mamba.yaml /tmp/mamba.yaml
# 安装conda环境
RUN micromamba install -y -n base -f /tmp/mamba.yaml && micromamba clean -a -y
# pip配置
RUN pip config set global.index-url https://pypi-1703563938750:504b6dbe8de1f29495ad7efc6012a42a08e9cb2b@zhu-ying-pypi.pkg.coding.net/kszy/pypi/simple
# 安装当前项目
ADD snakemake/ /opt/snakemake/
ADD jar/mitolib-0.1.2.jar /opt/conda/share/mitolib/mitolib-0.1.2.jar
ADD bin/mt_snv /opt/conda/bin/mt_snv
ADD bin/gvcf2vcf /opt/conda/bin/gvcf2vcf
ADD bin/germline_snv /opt/conda/bin/germline_snv
ADD bin/filter_vcf /opt/conda/bin/filter_vcf